Consolidate packaging dependency updates

[ihalatci]

Summary

• consolidate the latest unique updates from Dependabot PRs Bump jinja2 from 3.1.4 to 3.1.6 in /packaging_automation #394, Bump python-dotenv from 1.0.1 to 1.2.2 in /packaging_automation #395, Bump requests from 2.32.2 to 2.33.0 in /packaging_automation #397, Bump cryptography from 42.0.7 to 46.0.6 in /packaging_automation #398, Bump pygments from 2.18.0 to 2.20.0 in /packaging_automation #399, Bump pytest from 8.2.1 to 9.0.3 in /packaging_automation #400, Bump gitpython from 3.1.43 to 3.1.50 in /packaging_automation #404, Bump urllib3 from 2.2.1 to 2.7.0 in /packaging_automation #405, and Bump idna from 3.7 to 3.15 in /packaging_automation #406
• include the transitive cffi and typing-extensions updates required by cryptography
• keep the generated dependency lock internally consistent in a single file

Local validation

• resolver output matches pip-compile under Python 3.10
• installed package set passes dependency compatibility checks
• formatting check passes

CI will exercise the repository's Git- and Docker-backed workflows.